(222g) Modelling Microbial Microenvironments through Encapsulation of Synthetic Communities

In the field of microbiology, it is believed that less than 1% of microbes are presently known and have been studied. The inability to culture many microbes using traditional methods, such as plating or suspension, has led to a vast gap in our understanding of microbiomes. To overcome this challenge, we have developed a novel microfluidics system which enables us to encapsulate microbes in a semipermeable membrane on the scale of nanolitres, eliminating resource competition and effectively increasing cell communication of isolated microcolonies.

In this study, we are introducing a mock community developed in the nanocultures with five microbial species, including Pseudomonas aeruginosa, Escherichia coli Nissle 1917, Staphylococcus aureus, Streptococcus mutans and Candida albicans. We determine how population density differs when cells are cultured in nanocultures as opposed to culturing them in suspension in a flask. After an incubation period of 24 hours, the nanocultures are ruptured and DNA is isolated and sequenced from viable cells. 16srRNA sequencing allows us to determine the abundance of each species in both the nanocultures and flask cultures, thus we can determine how the species interact with each other under the constraints of each system. We anticipate that our microfluidics device will be able to capture unculturable microbes in future applications, from a variety of different environments, such as oral, gut, marine and soil, allowing for unknown microbe discovery, and furthermore, a more accessible and in-depth study of these unknown microbes.